I am an airline pilot, so please let me add something to the debate.
No-one runs laptop-based Maintenance Manuals, as these manuals are what the regulators audit regularly and/or use to prosecute licensed pilots/engineers if things go wrong. If they were electronic, they could be tampered with to cover things up, so they won't allow this.
The story is that this aircraft had a huge history of slat/flap problems that the central maintenance computer should have picked up and alerted the engineer controllers to bring it into the hangar and rectify. It did not and here is where the Trojans/OS issue is brought up.
The end result was that the pilots were trying to keep to schedule (long day, close to limits for duty time, etc) when the flaps would not extend. So they taxied back to the stand (more delay) for the engineer to rectify it. He over-rode some of the protections (and warnings) to get the job done, it appears. In their rush to recover the delay, the pilots forgot to run the flaps for take-off, there was no warning any more, people died.
So yes the ultimate blame lies with the pilots, but then the pilots are usually the last line of defence against systemic problems with the operation - an operation in this case possibly affected by Trojans! The Trojans didn't directly cause the crash, but crashes are usually caused by many little errors/conflicts and they were one part of that.
Just so you can enjoy your next flights, aircraft do not run Windows or similar commercial ("non-critical" OSes)